Hi Russell and all: I’ll respond here since the answer is related to the intended purpose of the VertLife mammal trees — i.e, capturing full uncertainty in node ages and phylogenetic relationships was one of the motivators for building the mammal trees in the way we did. This approach contrasts to wanting to obtain the single “best tree”, since methods of phylogenetic reconstruction will always just be approximations of the “true tree” anyway rather than ever being equal to that tree. To only use a single consensus tree in comparative phylogenetic analyses assumes that we know the true tree, which again, we don’t ever in an empirical context (only for simulations). Those points were summarized well by Huelsenbeck et al. (2000: http://science.sciencemag.org/content/288/5475/2349), but nevertheless are still not standard practice in PCMs.
To the point of AIC varying across the 100 trees, this is to be expected. Any 1 tree of 100 trees from the credible set is not very meaningful; the entire 100 trees need to be analyzed and then the estimate +/- SE from each tree can be summarized as a distribution of values. If the 95% CI on the distribution of values excludes your hypothesis, then you’ve learned something; if not, you accept the null hypothesis. See the animated gifs here (http://vertlife.org/data/mammals/) for a better conception of why this phylogenetic uncertainty is important to consider when doing model fitting or other PCMs. That said, if a single ‘best tree’ is the target, then the DNA-only MCC tree of 4098 species is a reasonable thing to analyze, more analogous to how mainstream phylogenetics has presented trees for re-use (https://github.com/n8upham/MamPhy_v1/blob/master/_DATA/MamPhy_fullPosterior_BDvr_DNAonly_4098sp_topoFree_NDexp_MCC_v2_target.tre). But again, while the MCC tree is appropriate, 1 of 100 trees from the credible set is not. Hope that helps. All the best, —nate ============================================================================== Nathan S. Upham, Ph.D. (he/him) Assistant Research Professor & Associate Curator of Mammals Arizona State University, School of Life Sciences, Biodiversity Knowledge Integration Center (BioKIC <https://biokic.asu.edu/>) ~> Check out the new Mammal Tree of Life <http://vertlife.org/data/mammals/> and the Mammal Diversity Database <https://mammaldiversity.org/> Research Associate, Yale University (Ecology and Evolutionary Biology) Research Associate, Field Museum of Natural History (Negaunee Integrative Research Center) Chair, Biodiversity Committee, American Society of Mammalogists Taxonomy Advisor, IUCN/SSC Small Mammal Specialist Group personal web: n8u.org | Google Scholar <https://scholar.google.com/citations?hl=en&user=zIn4NoUAAAAJ&view_op=list_works&gmla=AJsN-F6ybkfthmTdjTpow6sgMhWKn1EKcfNtmIF_wzZcev7yeHuEu5_aolFS85rWiVRHpiQgbwg43i6eS6kArrabLdFL4bntzUSRmlRP2CW4lbZqeEcColw> | ASU profile <https://isearch.asu.edu/profile/3682356> e: nathan.up...@asu.edu | Skype: nate_upham | Twitter: @n8_upham <https://twitter.com/n8_upham> ============================================================================= > On Jun 28, 2021, at 10:47 AM, Russell Engelman <neovenatori...@gmail.com> > wrote: > > Dear R-Sig-Phylo Mailing List, > > I ran into a rather unusual problem. I was doing an analysis using the > mammal trees from Upham et al. (2019) downloaded off of the VertLife site. > The model statistics for my data initially suggested that the OLS model was > better supported than a PGLS model based on Akaike Information Criterion > (AIC). The reviewers for the paper wanted me to add more taxa, so I > re-downloaded a set of trees from VertLife and reran the analysis, but when > I did I found that suddenly the AIC values for the PGLS equation were > dramatically different, to the point that it favored a Brownian PGLS model > over all other models. This was despite the fact that previously I found > that an OLS model and an OU model had a better model fit than a Brownian > model, and the other accuracy statistics of interest (like percent error, > this being a model intended for use in predicting new data) also found OLS > and OU models to fit better than a Brownian PGLS model. The regression line > for a Brownian model doesn't even fit the data at all due to being biased > by a basal clade. The model also has a high amount of phylogenetic inertia > which again would seemingly make an OU model a better option. > > I used drop.tip to remove the additional taxa to see if I could replicate > my previous results, but it turns out I still couldn't replicate the > results. That's when I realized what was causing the change in AIC values > wasn't the taxon selection, but the tree I was using. If I used the old > VertLife tree I could replicate the results, but the new VertLife tree > produced radically different results despite using the same tips. So what I > decided to do is rerun the analysis for all 100 trees I had available, and > it turned out there was a massive amount of variation in AIC depending on > what tree was chosen. I tried including an html data printout to show the > precise results and how I got them, but I couldn't attach them because the > mailer daemon kept saying they were too large. The AIC values between trees > vary by almost 200 points after excluding extreme outliers, when model > differences of 2 or more are often considered to represent statistically > detectable differences. The unusually low AIC I got when I first ran the > analysis happened to be because the first tree in the 100 trees merely > happened to produce a lower-than-average AIC than the whole sample. The > average AIC out of the 100 trees was higher than for the OLS model, which > again makes sense given the distribution of the data. > > However, and this is where my problem comes in, how do I make appropriate > model selections for PGLS if there is such a massive amount of variation in > AIC? Especially given that between the trees in the sample there is enough > variation that it can cause one model to be favored over another? Just > picking one tree and going with that seems counterintuitive, because it's > not very objective and theoretically someone could pick a specific tree to > get the results they want, or accidentally pick a tree that might support > the wrong model as seen here. On top of that the tree topologies are more > or less identical: the same 404 taxa are present in all trees and the trees > have nearly identical topologies, the only real differences between trees > are branch lengths. But given this, how can I justify which AIC value I > report, which in turn means which model is best supported? > > I did try looking at the phylo_lm function in the sensiphy package, but > that function doesn't seem to provide any method of performing model > selection between different regression models. It does seemingly report > AIC, but the AIC the function reported was dramatically different from the > aic I got using the gls function in ape and nlme. > > Sincerely, > Russell > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-phylo__;!!IKRxdwAv5BmarQ!J5VHDyumBg-_TLx239V3qrIJkgNlKLzuB6l9A_5abdDzeSOOXpHUKardHpGvRdojLg$ > > Searchable archive at > https://urldefense.com/v3/__http://www.mail-archive.com/r-sig-phylo@r-project.org/__;!!IKRxdwAv5BmarQ!J5VHDyumBg-_TLx239V3qrIJkgNlKLzuB6l9A_5abdDzeSOOXpHUKardHpF9l3tadg$ > [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
